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Table S1. List of Polyommatus icarus and Papilio machaon sequences used in this study apart from the Romanian dataset in Dincă et al. (2011a).

Table S2. GMYC results for the entire dataset and using different phylogenetic approaches.

Table S3. GMYC results for the five family trees using different phylogenetic approaches.

Table S4. Cases of GMYC failure (species that are either split or lumped) when analysing the entire dataset.

Table S5. GMYC results for the five family genealogies including all surveyed specimens and using BEAST with a coalescent prior and a strict molecular clock.

Table S6. Statistics for the GMYC best-fit and other models (within dAICc = 3) for a BEAST tree with a coalescent prior and a strict molecular clock.

Table S7. Comparison between GMYC number of entities for the full family tree and each significant subtree.

Table S8. Among the species that were recovered as an entity when using familylevel trees, those displaying the highest intra-specific divergence (p-distance > 0·5%) were used to test for the importance of intermediate haplotypes.

Figure S1. Probabilities (at nodes) that all tips nested within a node exist in a GMYC cluster according to model-averaged GMYC predictions.

Figure S2. Family trees with numbers assigned to nodes (corresponding to those of Table S6) and arrows indicating nodes that are significant for the GMYC model.

Figure S3. Plots showing the number of haplotypes vs. the (a) number of populations and (b) number of specimens for each of the species in the dataset.

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